Package: binneR 2.6.4

Jasen Finch

binneR: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry

A spectral binning approach for flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) metabolome fingerprinting data. The methodology for this approach is outlined in Finch et al. (2022) <doi:10.1007/s11306-022-01923-6>.

Authors:Jasen Finch [aut, cre]

binneR_2.6.4.tar.gz
binneR_2.6.4.zip(r-4.7)binneR_2.6.4.zip(r-4.6)binneR_2.6.4.zip(r-4.5)
binneR_2.6.4.tgz(r-4.6-any)binneR_2.6.4.tgz(r-4.5-any)
binneR_2.6.4.tar.gz(r-4.7-any)binneR_2.6.4.tar.gz(r-4.6-any)
binneR_2.6.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
binneR/json (API)

# Install 'binneR' in R:

install.packages('binneR', repos = c('https://aberhrml.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aberhrml/binner/issues

Pkgdown/docs site:https://aberhrml.github.io

On CRAN:

massspectrometry metabolomics fie-hrms fingerprinting high-resolution-mass-spectrometry mass-spectrometry spectral-binning

3.34 score 4 stars 11 scripts 24 downloads 28 exports 51 dependencies

Last updated from:98b89b29b5. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	198
source / vignettes	OK	219
linux-release-x86_64	NOTE	246
macos-release-arm64	NOTE	107
macos-oldrel-arm64	NOTE	107
windows-devel	NOTE	135
windows-release	NOTE	144
windows-oldrel	NOTE	141
wasm-release	OK	170

Exports:%>%accurateData binnedData binneRlyse binningParameters binParameters cls cls<-creationDate detectInfusionScans detectParameters filePaths plan plotBin plotCentrality plotChromatogram plotChromFromFile plotFingerprint plotPurity plotTIC readBinningParameters readFiles sampleInfo scans scans<-show singleSample version

Dependencies:Biobase BiocGenerics biocmake cli codetools cpp11 crayon digest dir.expiry dplyr farver filelock furrr future generics ggplot2 ggthemes globals glue gtable isoband labeling lifecycle listenv lubridate magrittr mzR ncdf4 parallelly pillar pkgconfig ProtGenerics purrr R6 RColorBrewer Rcpp Rhdf5lib rlang S7 scales stringi stringr tibble tidyr tidyselect timechange utf8 vctrs viridisLite withr yaml

binneR

Rendered frombinneR.Rmdusingknitr::rmarkdown

Last update: 2021-09-29
Started: 2018-07-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Spectral binning analysis class	Binalysis-class
Perform spectral binning	binneRlyse
Set spectral binning parameters	binParameters
Spectral binning parameters class	BinParameters-class
Detect infusion profile scan range	detectInfusionScans
Detect suitable spectral binning parameters	detectParameters
Plot a spectral bin feature	plotBin plotBin,Binalysis-method
Plot bin centrality histogram	plotCentrality plotCentrality,Binalysis-method
Plot an infusion profile chromatogram	plotChromatogram plotChromatogram,Binalysis-method
Plot an infusion profile chromatogram from a file	plotChromFromFile
Plot a fingerprint mass spectrum	plotFingerprint plotFingerprint,Binalysis-method
Plot bin purity histogram	plotPurity plotPurity,Binalysis-method
Plot sample total ion counts	plotTIC plotTIC,Binalysis-method
Read binning parameters from file	readBinningParameters
Read and process mulitple data files	readFiles
Get and set spectral binning parameters	cls cls,BinParameters-method cls<- cls<-,BinParameters-method scans scans,BinParameters-method scans<- scans<-,BinParameters-method
Show methods for spectral binning classes	show,Binalysis-method show,BinParameters-method
Perform single sample spectral binning	singleSample
Binalysis class get methods	accurateData accurateData,Binalysis-method binnedData binnedData,Binalysis-method binningParameters binningParameters,Binalysis-method creationDate creationDate,Binalysis-method filePaths filePaths,Binalysis-method sampleInfo sampleInfo,Binalysis-method version version,Binalysis-method